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Merging FASTQ (-e)

Merge the FASTQ files of multiple Runs into one file per Experiment (ex), Sample (sa), or Study (st).

adaptiseq -i SRX003906 -g -e ex

Most Experiments contain a single Run, but some span several (e.g. SRX003906, CRX020217). -e merges them in a consistent order so paired-end _1/_2 files stay aligned.

  • -e ex — merge all FASTQ of the same Experiment. Accepts ERX, DRX, SRX, CRX.
  • -e sa — merge all FASTQ of the same Sample. Accepts ERS, DRS, SRS, SAMC, GSM.
  • -e st — merge all FASTQ of the same Study. Accepts ERP, DRP, SRP, CRA.

Output:

  • single-end → SRX*.fastq.gz
  • paired-end → SRX*_1.fastq.gz and SRX*_2.fastq.gz

Note 1 -e cannot be used when the input accession is a Run ID. adaptiSeq merges gzip-compressed and uncompressed FASTQ, but not BAM or tar.gz files.

Note 2 When an Experiment has one Run and the Run's files share its prefix, adaptiSeq renames them directly to SRX*_1.fastq.gz / SRX*_2.fastq.gz. When a Run's files use different prefixes (e.g. CRX006713/CRR007192), they are renamed as SRX*_<original_filename>.

Note 3 Merge logic is deterministic — the same inputs produce the same merged bytes. adaptiSeq's engine changes only how the per-Run files are fetched, never their contents.